# ClioDeck Wiki

ClioDeck is an Electron + React + TypeScript desktop app for historians, covering the full research cycle **explore → brainstorm → write → export**. Local-first, RAG-powered, with Zotero / Tropy / Obsidian integrations and full MCP support (client + server).

This wiki is the user-facing reference. For internal engineering notes, see `docs/` in the repository.

> **RC4 is out.** A stabilisation candidate: three audits were run over
> everything RC3 changed, and their findings fixed. Most of what they found
> did not crash — it produced wrong results silently, including two defects
> that removed text from an exported book. Book settings, the manuscript
> corpus and several other features also gained the interfaces they lacked.
> See the [RC4 Release Notes](./3.4-RC4-Release-Notes.md).

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## Getting Started

- [Getting Started](./1.0-Getting-Started.md) — from a fresh install to your first chapter.
- [ClioDeck Installation (overview)](./1.-ClioDeck-Installation.md)
- [Installation — Linux](./1.1-ClioDeck-Installation-‐-Linux.md)
- [Installation — macOS](./1.2-ClioDeck-Installation-‐-macOS.md)
- [Keyboard Shortcuts](./1.4-Keyboard-Shortcuts.md)
- [Features](./Features.md) — the full feature list.

## Writing

- [The Editor](./1.16-The-Editor.md) — live markdown rendering, footnotes, citations, front matter, AI proposals.
- [Books and Chapters](./1.15-Books-and-Chapters.md) — multi-file manuscripts, chapter navigator, outline, book-wide tools, book settings.
- [Export Guide](./1.10-Export-Presentations.md) — PDF, Word, presentations (reveal.js and Beamer), and book scope.
- [Word Templates](./1.3-Guide-for-Using-Word-Templates.md)

## User Guides

### Sources & integrations

- [Zotero Integration Guide](./1.5-Zotero-Integration-Guide.md) — bibliography sync, PDF download, batch indexing.
- [Tropy Integration Guide](./1.6-Tropy-Integration-Guide.md) — primary sources (archives), OCR, transcription.
- [Obsidian Vault Guide](./1.14-Obsidian-Vault-Guide.md) — point ClioDeck at an Obsidian vault folder and use it as a RAG source.
- [Archive Connectors Guide](./1.13-Archive-Connectors-Guide.md) — Gallica (BnF), HAL (CCSD), Europeana.

### Working with the corpus

- [Embedded LLM Guide](./1.7-Embedded-LLM-Guide.md) — running models locally via Ollama or the bundled llama.cpp.
- [Corpus Analysis Guide](./1.8-Corpus-Analysis-Guide.md) — knowledge graph, textometrics, similarity finder.
- [Similarity Finder — architecture note](./FEATURE_SIMILARITY_FINDER.md) — implementation detail behind the guide above: caching, default values, provider wiring.
- [Journal and History](./1.9-Journal-and-History.md) — research journal, chat history, and the separate AI usage journal.

### The assistant & extensibility

- [Brainstorm Mode Guide](./1.11-Brainstorm-Mode-Guide.md) — the assistant: agent loop, MCP tools, project context. Since RC3 it is the *same* component wherever you open it in the app.
- [MCP Integration Guide](./1.12-MCP-Integration-Guide.md) — both directions: external MCP servers consumed from ClioDeck, and ClioDeck's own MCP server exposed to Claude Desktop / Claude Code.

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## Technical

- [Technical Architecture](./2.-Technical-Architecture.md)
- [Build and Deployment Guide](./2.1-Build-and-Deployment-Guide.md)
- [Logging System](./2.3-Logging-System.md)

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## Releases

- [RC4 Release Notes](./3.4-RC4-Release-Notes.md) — **current** (second audit cycle: silent wrong results fixed, missing interfaces added, full translation, security hardening).
- [RC3 Release Notes](./3.3-RC3-Release-Notes.md) — new editor, books in chapters, unified assistant, manuscript as a RAG corpus, three audits.
- [RC2 Release Notes](./3.2-RC2-Release-Notes.md) — ClioBrain fusion, MCP, archive connectors, Obsidian vault.
- Archive: [BETA 2 Release Notes](./_archive/3.1-BETA-2-Release-Notes.md), [Implementation Plan v1.0](./_archive/3.-Implementation-Plan-‐-ClioDeck-v1.0.md).

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## Ethics

- [Ethics](./4.-Ethics.md)
- [Environmental Cost of AI-Assisted Development](./4.1-Environmental-Costof-the-AI‐Assisted-Development-ClioDeck.md)